How to run velvet with OPENMP

Just few steps to make velvet working for de novo genome assembly using multiple CPU cores:

1) Download the latest version of velvet from
2) $ tar -xzvf velvet_1.2.10.tgz
3) $ cd velvet_1.2.10
4) Edit the Makefile to compile with a higher Kmer length and enable longsequences for contigs longer than 32kb:

$ vim Makefile


5) Install with sudo apt-get install some required packages: gcc, make, zlib1g-dev, bioperl
6) Compile velvet for multi-threaded use

$ make ‚OPENMP=1‘

Now you can run velveth:

$ velveth _outDir 31 -shortPaired -separate -fastq -file1.fq -file2.fq

and velvetg:

$ velvetg _outDir -expCov auto -cov_cutoff auto -min_contig_lgth 200 -ins_length 200 -amosfile yes -read_trkg yes


Written by: Heider